title: Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps.
abstract: Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
authors.affiliation: ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Fischer
authors.forename: Christian
authors.initials: C
authors.lastname: Rellstab
authors.forename: Andrew
authors.initials: A
authors.lastname: Tedder
authors.forename: Stefan
authors.initials: S
authors.lastname: Zoller
authors.forename: Felix
authors.initials: F
authors.lastname: Gugerli
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
authors.forename: Rolf
authors.initials: R
authors.lastname: Holderegger
authors.forename: Alex
authors.initials: A
authors.lastname: Widmer
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D002980:Climate; D018744:DNA, Plant / Q000235:genetics; D017753:Ecosystem; D063990:Gene Ontology; D017343:Genes, Plant; D005828:Genetics, Population; D023281:Genomics / Q000379:methods; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013557:Switzerland
chemical_list: D018744:DNA, Plant
keywords: Pool-Seq; adaptation; environmental association; genome resequencing; pooled sequencing; population genomics